Variant report

Variant	nsv1062461
Chromosome Location	chr20:1570740-1599142
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr20:1597810-1598006	K562	blood:	n/a	n/a
2	CEBPB	chr20:1596225-1596242	HepG2	liver:	n/a	n/a
3	CTCF	chr20:1583954-1584054	GM19239	blood:	n/a	chr20:1583996-1584006
4	CTCF	chr20:1594081-1594153	LNCaP	prostate:	n/a	n/a
5	CTCF	chr20:1595313-1595408	GM12878	blood:	n/a	n/a
6	CTCF	chr20:1583923-1584071	GM12891	blood:	n/a	chr20:1583996-1584006
7	CTCF	chr20:1595316-1595438	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr20:1585205-1585266	GM10248	blood:	n/a	n/a
9	CTCF	chr20:1583993-1584014	H1-hESC	embryonic stem cell:	n/a	chr20:1583996-1584006
10	CTCF	chr20:1583918-1584066	GM12878	blood:	n/a	chr20:1583996-1584006
11	CTCF	chr20:1583938-1584013	HUVEC	blood vessel:	n/a	chr20:1583996-1584006
12	CTCF	chr20:1589816-1589866	NHEK	skin:	n/a	n/a
13	CTCF	chr20:1583950-1584135	GM12878	blood:	n/a	chr20:1583996-1584006
14	CTCF	chr20:1583974-1584038	GM10266	blood:	n/a	chr20:1583996-1584006
15	CTCF	chr20:1593027-1593071	K562	blood:	n/a	n/a
16	E2F4	chr20:1596569-1596779	MCF10A-Er-Src	breast:	n/a	n/a
17	EBF1	chr20:1575968-1576160	GM12878	blood:	n/a	n/a
18	EBF1	chr20:1576059-1576210	GM12878	blood:	n/a	n/a
19	ELF1	chr20:1575954-1576254	GM12878	blood:	n/a	chr20:1576167-1576178
20	EP300	chr20:1597685-1598216	SK-N-SH_RA	brain:	n/a	n/a
21	EP300	chr20:1597667-1598072	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr20:1597694-1598043	Hela-S3	cervix:	n/a	n/a
23	FOS	chr20:1597654-1598180	HUVEC	blood vessel:	n/a	n/a
24	GATA2	chr20:1597568-1598284	HUVEC	blood vessel:	n/a	n/a
25	GATA3	chr20:1597872-1598067	SH-SY5Y	brain:	n/a	n/a
26	GATA3	chr20:1597619-1598351	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr20:1597682-1598321	SK-N-SH	brain:	n/a	n/a
28	IKZF1	chr20:1597593-1597902	GM12878	blood:	n/a	n/a
29	JUN	chr20:1597585-1598235	HUVEC	blood vessel:	n/a	n/a
30	JUND	chr20:1596140-1596296	HepG2	liver:	n/a	n/a
31	JUND	chr20:1597646-1598261	SK-N-SH	brain:	n/a	n/a
32	MAFF	chr20:1593355-1593403	HepG2	liver:	n/a	n/a
33	MAFK	chr20:1597082-1597111	HepG2	liver:	n/a	n/a
34	MAFK	chr20:1593290-1593446	HepG2	liver:	n/a	n/a
35	MAFK	chr20:1593238-1593539	HepG2	liver:	n/a	n/a
36	MAFK	chr20:1596956-1597144	HepG2	liver:	n/a	n/a
37	MYC	chr20:1597861-1597864	HUVEC	blood vessel:	n/a	n/a
38	MYC	chr20:1599129-1601288	NB4	blood:	n/a	n/a
39	MYC	chr20:1586165-1586228	H1-hESC	embryonic stem cell:	n/a	n/a
40	NFIC	chr20:1597634-1598179	SK-N-SH	brain:	n/a	n/a
41	PBX3	chr20:1597719-1598151	SK-N-SH	brain:	n/a	n/a
42	PBX3	chr20:1597746-1598208	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr20:1588361-1588475	GM12878	blood:	n/a	n/a
44	POLR2A	chr20:1597821-1597973	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr20:1589161-1589254	K562	blood:	n/a	n/a
46	POLR2A	chr20:1597578-1598200	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr20:1597649-1598301	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr20:1589549-1589563	GM12878	blood:	n/a	n/a
49	POLR2A	chr20:1571059-1571375	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr20:1597696-1598034	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:1578550-1578600	K562	blood:	n/a
2	chr20:1578550-1578600	RPTEC	kidney:	n/a
3	chr20:1578550-1578600	GM12892	blood:	n/a
4	chr20:1578550-1578600	HPAEpiC	pulmonary alveolar:	n/a
5	chr20:1578550-1578600	HAEpiC	amniotic membrane:	n/a
6	chr20:1578550-1578600	ECC-1	luminal epithelium:	n/a
7	chr20:1578550-1578600	HepG2	liver:	n/a
8	chr20:1578550-1578600	SAEC	small airway:	n/a
9	chr20:1578550-1578600	HCT-116	colon:	n/a
10	chr20:1578550-1578600	GM12891	blood:	n/a
11	chr20:1578550-1578600	SK-N-SH	brain:	n/a
12	chr20:1578550-1578600	GM12878	blood:	n/a
13	chr20:1578550-1578600	CMK	blood:	n/a
14	chr20:1578550-1578600	PFSK-1	brain:	n/a
15	chr20:1578550-1578600	GM06990	blood:	n/a
16	chr20:1578550-1578600	LNCaP	prostate:	n/a
17	chr20:1578550-1578600	NHDF-neo	bronchial:	n/a
18	chr20:1578550-1578600	Hepatocyte	liver:	n/a
19	chr20:1578550-1578600	T-47D	breast:	n/a
20	chr20:1578550-1578600	HUVEC	blood vessel:	n/a
21	chr20:1578550-1578600	HCM	heart:	n/a
22	chr20:1578550-1578600	AG04449	skin:	fetal
23	chr20:1578550-1578600	ProgFib	skin:	n/a
24	chr20:1578550-1578600	NT2-D1	testis:	n/a
25	chr20:1578550-1578600	BE2_C	brain:	n/a
26	chr20:1578550-1578600	NHBE	bronchial:	n/a
27	chr20:1578550-1578600	PrEC	prostate:	n/a
28	chr20:1578550-1578600	HRCEpiC	kidney:	n/a
29	chr20:1578550-1578600	HCPEpiC	choroid plexus:	n/a
30	chr20:1578550-1578600	NH-A	brain:	n/a
31	chr20:1578550-1578600	HRPEpiC	eye:	n/a
32	chr20:1578550-1578600	Jurkat	blood:	n/a
33	chr20:1578550-1578600	MCF10A-Er-Src	breast:	n/a
34	chr20:1578550-1578600	SK-N-MC	brain:	n/a
35	chr20:1578550-1578600	Hela-S3	cervix:	n/a
36	chr20:1578550-1578600	PANC-1	pancreas:	n/a
37	chr20:1578550-1578600	AoSMC	blood vessel:	n/a
38	chr20:1578550-1578600	U87	brain:	n/a
39	chr20:1578550-1578600	SKMC	muscle:	n/a
40	chr20:1578550-1578600	NB4	blood:	n/a
41	chr20:1578550-1578600	HMEC	breast:	n/a
42	chr20:1578550-1578600	ovcar-3	ovarian:	n/a
43	chr20:1578550-1578600	AG09309	skin:	n/a
44	chr20:1578550-1578600	GM19239	blood:	n/a
45	chr20:1578550-1578600	AG09319	gingival:	n/a
46	chr20:1578550-1578600	MCF-7	breast:	n/a
47	chr20:1578550-1578600	IMR90	lung:	fetal
48	chr20:1578550-1578600	HNPCEpiC	eye:	n/a
49	chr20:1578550-1578600	SK-N-SH_RA	brain:	n/a
50	chr20:1578550-1578600	HL-60	blood:	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNPH-4	chr20:1572038-1572494	NONHSAT078121
2	lnc-SNPH-5	chr20:1574682-1577118	ucscGeneNc_uc002wfp_1

No data

Variant related genes	Relation type
SIRPB1	TF binding region
ENSG00000260861	TF binding region
ENSG00000271523	TF binding region
SIRPB1	CpG island
ENSG00000260861	CpG island
ENSG00000271523	CpG island

Extended variants
information (count: 580 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:580 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553089601	chr20:1571442-1571443	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs574624116	chr20:1571446-1571447	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs542003075	chr20:1571450-1571451	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs556880105	chr20:1571467-1571468	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs111962716	chr20:1571490-1571491	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs201390207	chr20:1571545-1571546	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs113296065	chr20:1571547-1571548	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs140979173	chr20:1571863-1571864	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs3859626	chr20:1571874-1571875	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs192105963	chr20:1571885-1571886	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs528444095	chr20:1571899-1571900	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs540272302	chr20:1571920-1571921	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs561845873	chr20:1572018-1572019	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs529373689	chr20:1572188-1572189	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs145705854	chr20:1572256-1572257	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs1883935	chr20:1572374-1572375	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs6074855	chr20:1572408-1572409	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs372514247	chr20:1572585-1572586	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs111622289	chr20:1572957-1572958	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs184869554	chr20:1573092-1573093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188136308	chr20:1573164-1573165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs112066061	chr20:1573174-1573175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs146169245	chr20:1573253-1573254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs552082660	chr20:1573347-1573348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs192650290	chr20:1573761-1573762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs534589304	chr20:1573960-1573961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs184204353	chr20:1574057-1574058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs553050433	chr20:1574212-1574213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs568115302	chr20:1574304-1574305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs188349613	chr20:1574368-1574369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs192384927	chr20:1574521-1574522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs184937736	chr20:1574591-1574592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs575368533	chr20:1574651-1574652	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs189069759	chr20:1574745-1574746	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs569937413	chr20:1574837-1574838	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs111574569	chr20:1574845-1574846	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs181887031	chr20:1574853-1574854	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs557614176	chr20:1575172-1575173	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs138889344	chr20:1575178-1575179	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs540189968	chr20:1575187-1575188	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs141347807	chr20:1575211-1575212	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs574048167	chr20:1575282-1575283	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs143534612	chr20:1575588-1575589	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs148014484	chr20:1575635-1575636	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs141673124	chr20:1576147-1576148	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs533348633	chr20:1576181-1576182	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs552046003	chr20:1576233-1576234	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs560762366	chr20:1576274-1576275	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs527992907	chr20:1576281-1576282	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs546578802	chr20:1576346-1576347	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Glioblastoma multiforme	22286061	CNVD
Hepatocellular carcinoma	22174799	CNVD
Colorectal cancer	19455253	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17603634	CNVD
Colorectal cancer	19359472	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Intracranial aneurysm	16715129	CNVD
Colorectal cancer	16774939	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	17363583	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Lung cancer	18438408	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1560000-1579200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr20:1569400-1571000	Enhancers	Primary T cells from cord blood	blood
3	chr20:1569400-1572600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:1569800-1587000	Weak transcription	Spleen	Spleen
5	chr20:1570000-1570800	Enhancers	Dnd41	blood
6	chr20:1570400-1572600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr20:1570400-1599800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr20:1571000-1599000	Weak transcription	Primary T cells from cord blood	blood
9	chr20:1572600-1575400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr20:1572600-1575600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr20:1575400-1576000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr20:1575600-1577000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr20:1575800-1576400	Enhancers	Primary B cells from peripheral blood	blood
14	chr20:1576000-1576800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr20:1576800-1577400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr20:1577000-1578000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr20:1577400-1578400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr20:1578000-1584200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr20:1578400-1579000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr20:1578400-1585000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr20:1578600-1579000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:1579000-1581000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:1579200-1580000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:1579800-1580600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:1580000-1591400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:1581000-1582000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:1584200-1590200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr20:1585000-1590000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr20:1588000-1589800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr20:1589600-1600000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr20:1589800-1593600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr20:1590000-1590600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr20:1590200-1592600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr20:1590600-1593200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr20:1591400-1592400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr20:1592400-1599200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr20:1592600-1594600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr20:1593200-1594400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr20:1593600-1594400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr20:1594400-1595200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr20:1594400-1598800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr20:1594600-1597200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr20:1595200-1595400	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr20:1595400-1596400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
45	chr20:1595800-1597200	Enhancers	Primary B cells from cord blood	blood
46	chr20:1596400-1602400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr20:1596600-1598400	Enhancers	Hela-S3	cervix
48	chr20:1596600-1599400	Enhancers	HUVEC	blood vessel
49	chr20:1597000-1597400	Enhancers	Primary B cells from peripheral blood	blood
50	chr20:1597200-1597600	Flanking Active TSS	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links